The association between genetic markers and serological major histocompatibility complex (MHC) definition was studied in experimental White Leghorn lines selected for different immune traits. Different markers, three variable number tandem repeats (VNTRs) and 10 single nucleotide polymorphisms (SNPs), distributed along the MHC sequence were genotyped. Correlation between VNTR marker alleles and serology was studied in more than 800 animals and correspondence between SNP haplotypes and allele size was defined. A complete table of correspondence between VNTR allele sizes, SNP genotypes and serology was then drawn. This research shows that integrating new molecular tools can definitely help in MHC haplotype characterization and that, since the chicken MHC locus has been associated with disease resistance, these tools are becoming more and more needed for disease resistance and immunogenomics studies.